rs716349

Variant names:

• chr8-80866542-T-C
• rs716349
• NM_001033723.3:c.-22+8029A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033723.3(ZNF704):​c.-22+8029A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,250 control chromosomes in the GnomAD database, including 1,642 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1642 hom., cov: 32)
• Consequence: ZNF704 NM_001033723.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 1 publications found

Genes affected

ZNF704 (HGNC:32291): (zinc finger protein 704) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001033723.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF704	NM_001033723.3	MANE Select	c.-22+8029A>G		intron	N/A	NP_001028895.1
	ZNF704	NM_001367783.1		c.501+7002A>G		intron	N/A	NP_001354712.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF704	ENST00000327835.7	TSL:1 MANE Select	c.-22+8029A>G		intron	N/A	ENSP00000331462.3
	ZNF704	ENST00000519936.2	TSL:5	c.501+7002A>G		intron	N/A	ENSP00000427715.2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18432 AN: 152132 Hom.: 1634 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0888

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.121 AC: 18467 AN: 152250 Hom.: 1642 Cov.: 32 AF XY: 0.116 AC XY: 8662 AN XY: 74448

African (AFR) AF: 0.256 AC: 10616 AN: 41502

American (AMR) AF: 0.0885 AC: 1355 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0352 AC: 170 AN: 4828

European-Finnish (FIN) AF: 0.0475 AC: 504 AN: 10616

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5206 AN: 68020

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.0868 Hom.: 407

Bravo AF: 0.129

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.83
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs716349; hg19: chr8-81778777;